Sorry, but I'm afraid you may not get much help. The project is pretty much dead, and none of the original developers are around anymore to provide support. In fact, this same problem was reported in 2014, and no one had any solutions at that time. I suggested then that you could try posting at the Vegastrike forums, but that project is pretty much dead as well, so that probably won't help either.

Other than trying to manually edit the setup file by hand (vegastrike.config on Windows systems - YMMV), I don't know what else to tell you. Can you run the game at all?